[Bioperl-l] Bio::SimpleAlign problems

[Peter Stogios]

Hello,

I would like some help with Bio::SimpleAlign and Bio::AlignIO.

I am trying to do some VERY simple tasks but the AlignIO module is being
difficult in reading alignment files.  It does not seem to read many
formats correctly.

I am using the sample code included at the SimpleAlign documentation page.  
The code of interest is:

$str = Bio::AlignIO->new('-file' => 'testaln.aln');
$aln = $str->next_aln();
print $aln->no_residues, "\n";
print $aln->no_sequences, "\n";

I have tried loading ClustalX format version 1.81, ClustalW version 1.5, 
MSF format, and PHYLIP format, without having success.  I am sure the 
alignment files are in their correct formats, since other programs can 
read them.

Can someone please inform me what is the preferred format for reading by 
AlignIO and SimpleAlign?  Also, should I specify the format of the 
alignment in the Bio::AlignIO-->new line?

Thank you very much in advance,

Peter Stogios

-- 
____________________________________________________________
Peter Stogios               |  Ontario Cancer Institute
Graduate Student            |  Princess Margaret Hospital
G. Prive Lab                |  610 University Ave. Rm.7-207
Dept. of Medical Biophysics |  M5G 2M9
University of Toronto       |  (416) 946-2000 ex. 5615

pstogios at uhnres.utoronto.ca
http://xtal.uhnres.utoronto.ca/prive
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